1
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Karafoulidi-Retsou C, Katz S, Frielingsdorf S, Lenz O, Zebger I, Caserta G. A strong H-bond between a cysteine and the catalytic center of a [NiFe]-hydrogenase. Chem Commun (Camb) 2025; 61:5778-5781. [PMID: 40125578 DOI: 10.1039/d5cc00646e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
Abstract
Infrared spectroscopy at cryogenic temperatures was used to monitor protonation changes on an H+-accepting, nickel-coordinating active site cysteine of the H2/H+-cycling membrane-bound [NiFe]-hydrogenase from Cupriavidus necator. Surprisingly, we identified another cysteine in the outer coordination sphere forming a strong H-bond with a cysteine thiolate coordinating both nickel and iron of the catalytic center.
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Affiliation(s)
- Chara Karafoulidi-Retsou
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Stefan Frielingsdorf
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
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2
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Cabotaje P, Sekretareva A, Senger M, Huang P, Walter K, Redman HJ, Croy N, Stripp ST, Land H, Berggren G. Probing the Influence of the Protein Scaffold on H-Cluster Reactivity via Gain-of-Function Studies─Improved H 2 Evolution and O 2 Tolerance through Rational Design of [FeFe] Hydrogenase. J Am Chem Soc 2025; 147:4654-4666. [PMID: 39868705 PMCID: PMC11803613 DOI: 10.1021/jacs.4c17364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 01/14/2025] [Accepted: 01/15/2025] [Indexed: 01/28/2025]
Abstract
[FeFe] hydrogenases make up a structurally diverse family of metalloenzymes that catalyze proton/dihydrogen interconversion. They can be classified into phylogenetically distinct groups denoted A-G, which differ in structure and reactivity. Prototypical Group A hydrogenases have high turnover rates and remarkable energy efficiency. As compared to Group A enzymes, the putatively sensory Group D hydrogenase from Thermoanaerobacter mathranii (TamHydS) has a thousand-fold lower H2 evolution rate and a high overpotential requirement to drive catalysis (irreversible) but shows increased inhibitor tolerance. This divergence in structure and activity between hydrogenases makes them ideal models for studying second (active-site environment) and outer (e.g., substrate transport) coordination sphere effects on metal cofactors. Herein, we generated three TamHydS-based variants, each mimicking proposed key structural features of Group A hydrogenase: the "active site" (AS), "proton-transfer pathway" (PTP), and "combined" (CM = AS + PTP) variant. A fourth single-point variant, A137C, which introduces a proposed critical cysteine in the active site, was characterized as a reference. No change in isolation resulted in Group A-like behavior; i.e., no positive impact on catalytic performance was observed. The CM variant, however, showed increased H2 evolution activity but retained the overpotential requirement. Additionally, the CM variant improved the already relatively high stability of TamHydS against O2 and CO inhibition. These findings show that activity rates, (ir)reversibility, and susceptibility to gaseous inhibitors are decoupled. Moreover, the results highlight the importance of exploring hydrogenase diversity as a path toward understanding the structural factors that enable the outstanding catalytic properties of [FeFe] hydrogenases.
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Affiliation(s)
- Princess
R. Cabotaje
- Molecular
Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, P.O. Box 523, Uppsala SE-75120, Sweden
| | - Alina Sekretareva
- Molecular
Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, P.O. Box 523, Uppsala SE-75120, Sweden
| | - Moritz Senger
- Molecular
Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, P.O. Box 523, Uppsala SE-75120, Sweden
- Biochemistry,
Department of Chemistry, Biomedical Centre, Uppsala University, Uppsala SE-75120, Sweden
| | - Ping Huang
- Molecular
Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, P.O. Box 523, Uppsala SE-75120, Sweden
| | - Kaija Walter
- Molecular
Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, P.O. Box 523, Uppsala SE-75120, Sweden
| | - Holly J. Redman
- Molecular
Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, P.O. Box 523, Uppsala SE-75120, Sweden
| | - Nicholas Croy
- Molecular
Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, P.O. Box 523, Uppsala SE-75120, Sweden
| | - Sven T. Stripp
- Spectroscopy
and Biocatalysis, Institute of Chemistry, Universität Potsdam, Potsdam D-14476, Germany
| | - Henrik Land
- Molecular
Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, P.O. Box 523, Uppsala SE-75120, Sweden
| | - Gustav Berggren
- Molecular
Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, P.O. Box 523, Uppsala SE-75120, Sweden
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3
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Yarman A, Waffo AFT, Katz S, Bernitzky C, Kovács N, Borrero P, Frielingsdorf S, Supala E, Dragelj J, Kurbanoglu S, Neumann B, Lenz O, Mroginski MA, Gyurcsányi RE, Wollenberger U, Scheller FW, Caserta G, Zebger I. A Strep-Tag Imprinted Polymer Platform for Heterogenous Bio(electro)catalysis. Angew Chem Int Ed Engl 2024; 63:e202408979. [PMID: 38979660 DOI: 10.1002/anie.202408979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024]
Abstract
Molecularly imprinted polymers (MIPs) are artificial receptors equipped with selective recognition sites for target molecules. One of the most promising strategies for protein MIPs relies on the exploitation of short surface-exposed protein fragments, termed epitopes, as templates to imprint binding sites in a polymer scaffold for a desired protein. However, the lack of high-resolution structural data of flexible surface-exposed regions challenges the selection of suitable epitopes. Here, we addressed this drawback by developing a polyscopoletin-based MIP that recognizes recombinant proteins via imprinting of the widely used Strep-tag II affinity peptide (Strep-MIP). Electrochemistry, surface-sensitive IR spectroscopy, and molecular dynamics simulations were employed to ensure an utmost control of the Strep-MIP electrosynthesis. The functionality of this novel platform was verified with two Strep-tagged enzymes: an O2-tolerant [NiFe]-hydrogenase, and an alkaline phosphatase. The enzymes preserved their biocatalytic activities after multiple utilization confirming the efficiency of Strep-MIP as a general biocompatible platform to confine recombinant proteins for exploitation in biotechnology.
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Affiliation(s)
- Aysu Yarman
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476, Potsdam
- Molecular Biotechnology, Faculty of Science, Turkish-German University, Sahinkaya Cad. No. 86, Beykoz, Istanbul, 34820, Türkiye
| | - Armel F T Waffo
- Institut für Chemie, Technische Universität Berlin, PC 14 Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, PC 14 Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Cornelius Bernitzky
- Institut für Chemie, Technische Universität Berlin, PC 14 Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Norbert Kovács
- BME Lendület Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111, Budapest, Hungary
| | - Paloma Borrero
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476, Potsdam
| | - Stefan Frielingsdorf
- Institut für Chemie, Technische Universität Berlin, PC 14 Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Eszter Supala
- BME Lendület Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111, Budapest, Hungary
| | - Jovan Dragelj
- Institut für Chemie, Technische Universität Berlin, PC 14 Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Sevinc Kurbanoglu
- Faculty of Pharmacy, Department of Analytical Chemistry, Ankara University, Yenimahalle, Ankara, 06560, Turkey
| | - Bettina Neumann
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476, Potsdam
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, PC 14 Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Maria Andrea Mroginski
- Institut für Chemie, Technische Universität Berlin, PC 14 Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Róbert E Gyurcsányi
- BME Lendület Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111, Budapest, Hungary
- HUN-REN-BME Computation Driven Chemistry Research Group, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111, Budapest, Hungary
| | - Ulla Wollenberger
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476, Potsdam
| | - Frieder W Scheller
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476, Potsdam
| | - Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, PC 14 Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, PC 14 Straße des 17. Juni 135, 10623, Berlin, Germany
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4
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Fasano A, Fourmond V, Léger C. Outer-sphere effects on the O 2 sensitivity, catalytic bias and catalytic reversibility of hydrogenases. Chem Sci 2024; 15:5418-5433. [PMID: 38638217 PMCID: PMC11023054 DOI: 10.1039/d4sc00691g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024] Open
Abstract
The comparison of homologous metalloenzymes, in which the same inorganic active site is surrounded by a variable protein matrix, has demonstrated that residues that are remote from the active site may have a great influence on catalytic properties. In this review, we summarise recent findings on the diverse molecular mechanisms by which the protein matrix may define the oxygen tolerance, catalytic directionality and catalytic reversibility of hydrogenases, enzymes that catalyse the oxidation and evolution of H2. These mechanisms involve residues in the second coordination sphere of the active site metal ion, more distant residues affecting protein flexibility through their side chains, residues lining the gas channel and even accessory subunits. Such long-distance effects, which contribute to making enzymes efficient, robust and different from one another, are a source of wonder for biochemists and a challenge for synthetic bioinorganic chemists.
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Affiliation(s)
- Andrea Fasano
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
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5
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Schmidt A, Kalms J, Lorent C, Katz S, Frielingsdorf S, Evans RM, Fritsch J, Siebert E, Teutloff C, Armstrong FA, Zebger I, Lenz O, Scheerer P. Stepwise conversion of the Cys 6[4Fe-3S] to a Cys 4[4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase. Chem Sci 2023; 14:11105-11120. [PMID: 37860641 PMCID: PMC10583674 DOI: 10.1039/d3sc03739h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
The membrane-bound [NiFe]-hydrogenase of Cupriavidus necator is a rare example of a truly O2-tolerant hydrogenase. It catalyzes the oxidation of H2 into 2e- and 2H+ in the presence of high O2 concentrations. This characteristic trait is intimately linked to the unique Cys6[4Fe-3S] cluster located in the proximal position to the catalytic center and coordinated by six cysteine residues. Two of these cysteines play an essential role in redox-dependent cluster plasticity, which bestows the cofactor with the capacity to mediate two redox transitions at physiological potentials. Here, we investigated the individual roles of the two additional cysteines by replacing them individually as well as simultaneously with glycine. The crystal structures of the corresponding MBH variants revealed the presence of Cys5[4Fe-4S] or Cys4[4Fe-4S] clusters of different architecture. The protein X-ray crystallography results were correlated with accompanying biochemical, spectroscopic and electrochemical data. The exchanges resulted in a diminished O2 tolerance of all MBH variants, which was attributed to the fact that the modified proximal clusters mediated only one redox transition. The previously proposed O2 protection mechanism that detoxifies O2 to H2O using four protons and four electrons supplied by the cofactor infrastructure, is extended by our results, which suggest efficient shutdown of enzyme function by formation of a hydroxy ligand in the active site that protects the enzyme from O2 binding under electron-deficient conditions.
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Affiliation(s)
- Andrea Schmidt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics (CC2), Group Structural Biology of Cellular Signaling Charitéplatz 1 10117 Berlin Germany
| | - Jacqueline Kalms
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics (CC2), Group Structural Biology of Cellular Signaling Charitéplatz 1 10117 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Sagie Katz
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Stefan Frielingsdorf
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Johannes Fritsch
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Elisabeth Siebert
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Teutloff
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics (CC2), Group Structural Biology of Cellular Signaling Charitéplatz 1 10117 Berlin Germany
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6
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Harris TGAA, Heidary N, Frielingsdorf S, Rauwerdink S, Tahraoui A, Lenz O, Zebger I, Fischer A. Electrografted Interfaces on Metal Oxide Electrodes for Enzyme Immobilization and Bioelectrocatalysis. ChemElectroChem 2021. [DOI: 10.1002/celc.202100020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tomos G. A. A. Harris
- Albert-Ludwigs-Universität Freiburg Institut für Anorganische und Analytische Chemie Albertstr. 21 79104 Freiburg Germany
- Technische Universität Berlin Institut für Chemie, PC 14 Str. des 17. Juni 135 10623 Berlin Germany
| | - Nina Heidary
- Albert-Ludwigs-Universität Freiburg Institut für Anorganische und Analytische Chemie Albertstr. 21 79104 Freiburg Germany
- Technische Universität Berlin Institut für Chemie, PC 14 Str. des 17. Juni 135 10623 Berlin Germany
- Department of Chemistry Université de Montréal Roger-Gaudry Building Montreal, Quebec H3C 3J7 Canada
| | - Stefan Frielingsdorf
- Technische Universität Berlin Institut für Chemie, PC 14 Str. des 17. Juni 135 10623 Berlin Germany
| | - Sander Rauwerdink
- Paul-Drude-Institut für Festkörperelektronik Hausvogteiplatz 5–7 10117 Berlin Germany
| | - Abbes Tahraoui
- Paul-Drude-Institut für Festkörperelektronik Hausvogteiplatz 5–7 10117 Berlin Germany
| | - Oliver Lenz
- Technische Universität Berlin Institut für Chemie, PC 14 Str. des 17. Juni 135 10623 Berlin Germany
| | - Ingo Zebger
- Technische Universität Berlin Institut für Chemie, PC 14 Str. des 17. Juni 135 10623 Berlin Germany
| | - Anna Fischer
- Albert-Ludwigs-Universität Freiburg Institut für Anorganische und Analytische Chemie Albertstr. 21 79104 Freiburg Germany
- Technische Universität Berlin Institut für Chemie, PC 14 Str. des 17. Juni 135 10623 Berlin Germany
- Freiburger Materialforschungszentrum (FMF) Albert-Ludwigs-Universität Freiburg Stefan-Meier-Straße 21 79104 Freiburg Germany
- FIT Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte Technologien Georges-Köhler-Allee 105 79110 Freiburg Germany
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7
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Ruff A, Szczesny J, Vega M, Zacarias S, Matias PM, Gounel S, Mano N, Pereira IAC, Schuhmann W. Redox-Polymer-Wired [NiFeSe] Hydrogenase Variants with Enhanced O 2 Stability for Triple-Protected High-Current-Density H 2 -Oxidation Bioanodes. CHEMSUSCHEM 2020; 13:3627-3635. [PMID: 32339386 PMCID: PMC7497094 DOI: 10.1002/cssc.202000999] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/25/2020] [Indexed: 06/01/2023]
Abstract
Variants of the highly active [NiFeSe] hydrogenase from D. vulgaris Hildenborough that exhibit enhanced O2 tolerance were used as H2 -oxidation catalysts in H2 /O2 biofuel cells. Two [NiFeSe] variants were electrically wired by means of low-potential viologen-modified redox polymers and evaluated with respect to H2 -oxidation and stability against O2 in the immobilized state. The two variants showed maximum current densities of (450±84) μA cm-2 for G491A and (476±172) μA cm-2 for variant G941S on glassy carbon electrodes and a higher O2 tolerance than the wild type. In addition, the polymer protected the enzyme from O2 damage and high-potential inactivation, establishing a triple protection for the bioanode. The use of gas-diffusion bioanodes provided current densities for H2 -oxidation of up to 6.3 mA cm-2 . Combination of the gas-diffusion bioanode with a bilirubin oxidase-based gas-diffusion O2 -reducing biocathode in a membrane-free biofuel cell under anode-limiting conditions showed unprecedented benchmark power densities of 4.4 mW cm-2 at 0.7 V and an open-circuit voltage of 1.14 V even at moderate catalyst loadings, outperforming the previously reported system obtained with the [NiFeSe] wild type and the [NiFe] hydrogenase from D. vulgaris Miyazaki F.
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Affiliation(s)
- Adrian Ruff
- Analytical Chemistry—Center for Electrochemical Sciences (CES)Faculty of Chemistry and BiochemistryRuhr-University BochumUniversitätsstr. 15044780BochumGermany
| | - Julian Szczesny
- Analytical Chemistry—Center for Electrochemical Sciences (CES)Faculty of Chemistry and BiochemistryRuhr-University BochumUniversitätsstr. 15044780BochumGermany
| | - Maria Vega
- Facultat de BiociènciesUniversitat Autònoma de Barcelona (UAB)Carrer de la Vall Moronta08193BellaterraSpain
| | - Sonia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA)Universidade NOVA de LisboaAv. da República2780-157OeirasPortugal
| | - Pedro M. Matias
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA)Universidade NOVA de LisboaAv. da República2780-157OeirasPortugal
- Instituto de Biologia Experimental e Tecnológica (iBET)Apartado 122780-901OeirasPortugal
| | | | - Nicolas Mano
- CNRSCRPP, UMR 5031Univ. Bordeaux33600PessacFrance
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA)Universidade NOVA de LisboaAv. da República2780-157OeirasPortugal
| | - Wolfgang Schuhmann
- Analytical Chemistry—Center for Electrochemical Sciences (CES)Faculty of Chemistry and BiochemistryRuhr-University BochumUniversitätsstr. 15044780BochumGermany
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8
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Horch M, Schoknecht J, Wrathall SLD, Greetham GM, Lenz O, Hunt NT. Understanding the structure and dynamics of hydrogenases by ultrafast and two-dimensional infrared spectroscopy. Chem Sci 2019; 10:8981-8989. [PMID: 31762978 PMCID: PMC6857670 DOI: 10.1039/c9sc02851j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022] Open
Abstract
Hydrogenases are valuable model enzymes for sustainable energy conversion approaches using H2, but rational utilization of these base-metal biocatalysts requires a detailed understanding of the structure and dynamics of their complex active sites. The intrinsic CO and CN- ligands of these metalloenzymes represent ideal chromophores for infrared (IR) spectroscopy, but structural and dynamic insight from conventional IR absorption experiments is limited. Here, we apply ultrafast and two-dimensional (2D) IR spectroscopic techniques, for the first time, to study hydrogenases in detail. Using an O2-tolerant [NiFe] hydrogenase as a model system, we demonstrate that IR pump-probe spectroscopy can explore catalytically relevant ligand bonding by accessing high-lying vibrational states. This ultrafast technique also shows that the protein matrix is influential in vibrational relaxation, which may be relevant for energy dissipation from the active site during fast reaction steps. Further insights into the relevance of the active site environment are provided by 2D-IR spectroscopy, which reveals equilibrium dynamics and structural constraints imposed on the H2-accepting intermediate of [NiFe] hydrogenases. Both techniques offer new strategies for uniquely identifying redox-structural states in complex catalytic mixtures via vibrational quantum beats and 2D-IR off-diagonal peaks. Together, these findings considerably expand the scope of IR spectroscopy in hydrogenase research, and new perspectives for the characterization of these enzymes and other (bio-)organometallic targets are presented.
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Affiliation(s)
- Marius Horch
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Janna Schoknecht
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Solomon L D Wrathall
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , Oxford , OX110PE , UK
| | - Oliver Lenz
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Neil T Hunt
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
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9
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Harris TGAA, Heidary N, Kozuch J, Frielingsdorf S, Lenz O, Mroginski MA, Hildebrandt P, Zebger I, Fischer A. In Situ Spectroelectrochemical Studies into the Formation and Stability of Robust Diazonium-Derived Interfaces on Gold Electrodes for the Immobilization of an Oxygen-Tolerant Hydrogenase. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23380-23391. [PMID: 29943966 DOI: 10.1021/acsami.8b02273] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Surface-enhanced infrared absorption spectroscopy is used in situ to determine the electrochemical stability of organic interfaces deposited onto the surface of nanostructured, thin-film gold electrodes via the electrochemical reduction of diazonium salts. These interfaces are shown to exhibit a wide electrochemical stability window in both acetonitrile and phosphate buffer, far surpassing the stability window of thiol-derived self-assembled monolayers. Using the same in situ technique, the application of radical scavengers during the electrochemical reduction of diazonium salts is shown to moderate interface formation. Consequently, the heterogeneous charge-transfer resistance can be reduced sufficiently to enhance the direct electron transfer between an immobilized redox-active enzyme and the electrode. This was demonstrated for the oxygen-tolerant [NiFe] hydrogenase from the "Knallgas" bacterium Ralstonia eutropha by relating its electrochemical activity for hydrogen oxidation to the interface properties.
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Affiliation(s)
- Tomos G A A Harris
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
| | - Nina Heidary
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
| | - Jacek Kozuch
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Stefan Frielingsdorf
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Oliver Lenz
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
- FMF - Freiburger Materialforschungszentrum , Universität Freiburg , Stefan-Meier-Straße 21 , 79104 Freiburg , Germany
- FIT - Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte Technologien , Georges-Köhler-Allee 105 , 79110 Freiburg , Germany
| | - Maria-Andrea Mroginski
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Peter Hildebrandt
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Ingo Zebger
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Anna Fischer
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
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10
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Esmieu C, Raleiras P, Berggren G. From protein engineering to artificial enzymes - biological and biomimetic approaches towards sustainable hydrogen production. SUSTAINABLE ENERGY & FUELS 2018; 2:724-750. [PMID: 31497651 PMCID: PMC6695573 DOI: 10.1039/c7se00582b] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/31/2018] [Indexed: 06/09/2023]
Abstract
Hydrogen gas is used extensively in industry today and is often put forward as a suitable energy carrier due its high energy density. Currently, the main source of molecular hydrogen is fossil fuels via steam reforming. Consequently, novel production methods are required to improve the sustainability of hydrogen gas for industrial processes, as well as paving the way for its implementation as a future solar fuel. Nature has already developed an elaborate hydrogen economy, where the production and consumption of hydrogen gas is catalysed by hydrogenase enzymes. In this review we summarize efforts on engineering and optimizing these enzymes for biological hydrogen gas production, with an emphasis on their inorganic cofactors. Moreover, we will describe how our understanding of these enzymes has been applied for the preparation of bio-inspired/-mimetic systems for efficient and sustainable hydrogen production.
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Affiliation(s)
- C Esmieu
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - P Raleiras
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - G Berggren
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
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11
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Abstract
Obtaining abundant pure hydrogen by reduction of water has an important implication in the development of clean and renewable energy. Hence research focused on the development of non-noble metal based facile and energy efficient catalysts for proton reduction is on the rise. However, for practical utilization, it is necessary that these complexes function unabated in the presence of atmospheric oxygen and other common contaminants in abundant water sources. There has been very little activity towards the development of oxygen-tolerant hydrogen producing catalysts. This article aims to draw attention to this issue of oxygen sensitivity in the HER and highlights the development of a few air-stable HER catalysts (enzymatic as well as artificial) elaborating the challenges involved and the techniques discovered to overcome this significant deterrent to large-scale hydrogen production by electrolysis from abundant water sources.
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Affiliation(s)
- Biswajit Mondal
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A&2B Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, India.
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12
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Lenz O, Lauterbach L, Frielingsdorf S. O2-tolerant [NiFe]-hydrogenases of Ralstonia eutropha H16: Physiology, molecular biology, purification, and biochemical analysis. Methods Enzymol 2018; 613:117-151. [DOI: 10.1016/bs.mie.2018.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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13
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Nangle SN, Sakimoto KK, Silver PA, Nocera DG. Biological-inorganic hybrid systems as a generalized platform for chemical production. Curr Opin Chem Biol 2017; 41:107-113. [DOI: 10.1016/j.cbpa.2017.10.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 12/16/2022]
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14
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Laftsoglou T, Jeuken LJC. Supramolecular electrode assemblies for bioelectrochemistry. Chem Commun (Camb) 2017; 53:3801-3809. [PMID: 28317998 PMCID: PMC5436043 DOI: 10.1039/c7cc01154g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/14/2017] [Indexed: 12/03/2022]
Abstract
For more than three decades, the field of bioelectrochemistry has provided novel insights into the catalytic mechanisms of enzymes, the principles that govern biological electron transfer, and has elucidated the basic principles for bioelectrocatalytic systems. Progress in biochemistry, bionanotechnology, and our ever increasing ability to control the chemistry and structure of electrode surfaces has enabled the study of ever more complex systems with bioelectrochemistry. This feature article highlights developments over the last decade, where supramolecular approaches have been employed to develop electrode assemblies that increase enzyme loading on the electrode or create more biocompatible environments for membrane enzymes. Two approaches are particularly highlighted: the use of layer-by-layer assembly, and the modification of electrodes with planar lipid membranes.
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Affiliation(s)
- Theodoros Laftsoglou
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK.
| | - Lars J C Jeuken
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK.
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15
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Reeve HA, Ash PA, Park H, Huang A, Posidias M, Tomlinson C, Lenz O, Vincent KA. Enzymes as modular catalysts for redox half-reactions in H2-powered chemical synthesis: from biology to technology. Biochem J 2017; 474:215-230. [PMID: 28062838 PMCID: PMC5298933 DOI: 10.1042/bcj20160513] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/11/2016] [Accepted: 11/15/2016] [Indexed: 11/17/2022]
Abstract
The present study considers the ways in which redox enzyme modules are coupled in living cells for linking reductive and oxidative half-reactions, and then reviews examples in which this concept can be exploited technologically in applications of coupled enzyme pairs. We discuss many examples in which enzymes are interfaced with electronically conductive particles to build up heterogeneous catalytic systems in an approach which could be termed synthetic biochemistry We focus on reactions involving the H+/H2 redox couple catalysed by NiFe hydrogenase moieties in conjunction with other biocatalysed reactions to assemble systems directed towards synthesis of specialised chemicals, chemical building blocks or bio-derived fuel molecules. We review our work in which this approach is applied in designing enzyme-modified particles for H2-driven recycling of the nicotinamide cofactor NADH to provide a clean cofactor source for applications of NADH-dependent enzymes in chemical synthesis, presenting a combination of published and new work on these systems. We also consider related photobiocatalytic approaches for light-driven production of chemicals or H2 as a fuel. We emphasise the techniques available for understanding detailed catalytic properties of the enzymes responsible for individual redox half-reactions, and the importance of a fundamental understanding of the enzyme characteristics in enabling effective applications of redox biocatalysis.
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Affiliation(s)
- Holly A Reeve
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, OX1 3QR, U.K
| | - Philip A Ash
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, OX1 3QR, U.K
| | - HyunSeo Park
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, OX1 3QR, U.K
| | - Ailun Huang
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, OX1 3QR, U.K
| | - Michalis Posidias
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, OX1 3QR, U.K
| | - Chloe Tomlinson
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, OX1 3QR, U.K
| | - Oliver Lenz
- Department of Chemistry, Technische Universität Berlin, Berlin 10623, Germany
| | - Kylie A Vincent
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, OX1 3QR, U.K.
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16
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Methylacidiphilum fumariolicum SolV, a thermoacidophilic 'Knallgas' methanotroph with both an oxygen-sensitive and -insensitive hydrogenase. ISME JOURNAL 2016; 11:945-958. [PMID: 27935590 PMCID: PMC5364354 DOI: 10.1038/ismej.2016.171] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/26/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022]
Abstract
Methanotrophs play a key role in balancing the atmospheric methane concentration. Recently, the microbial methanotrophic diversity was extended by the discovery of thermoacidophilic methanotrophs belonging to the Verrucomicrobia phylum in geothermal areas. Here we show that a representative of this new group, Methylacidiphilum fumariolicum SolV, is able to grow as a real 'Knallgas' bacterium on hydrogen/carbon dioxide, without addition of methane. The full genome of strain SolV revealed the presence of two hydrogen uptake hydrogenases genes, encoding an oxygen-sensitive (hup-type) and an oxygen-insensitive enzyme (hhy-type). The hhy-type hydrogenase was constitutively expressed and active and supported growth on hydrogen alone up to a growth rate of 0.03 h-1, at O2 concentrations below 1.5%. The oxygen-sensitive hup-type hydrogenase was expressed when oxygen was reduced to below 0.2%. This resulted in an increase of the growth rate to a maximum of 0.047 h-1, that is 60% of the rate on methane. The results indicate that under natural conditions where both hydrogen and methane might be limiting strain SolV may operate primarily as a methanotrophic 'Knallgas' bacterium. These findings argue for a revision of the role of hydrogen in methanotrophic ecosystems, especially in soil and related to consumption of atmospheric methane.
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17
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Liu C, Colón BC, Ziesack M, Silver PA, Nocera DG. Water splitting-biosynthetic system with CO₂ reduction efficiencies exceeding photosynthesis. Science 2016; 352:1210-3. [PMID: 27257255 DOI: 10.1126/science.aaf5039] [Citation(s) in RCA: 491] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/22/2016] [Indexed: 01/18/2024]
Abstract
Artificial photosynthetic systems can store solar energy and chemically reduce CO2 We developed a hybrid water splitting-biosynthetic system based on a biocompatible Earth-abundant inorganic catalyst system to split water into molecular hydrogen and oxygen (H2 and O2) at low driving voltages. When grown in contact with these catalysts, Ralstonia eutropha consumed the produced H2 to synthesize biomass and fuels or chemical products from low CO2 concentration in the presence of O2 This scalable system has a CO2 reduction energy efficiency of ~50% when producing bacterial biomass and liquid fusel alcohols, scrubbing 180 grams of CO2 per kilowatt-hour of electricity. Coupling this hybrid device to existing photovoltaic systems would yield a CO2 reduction energy efficiency of ~10%, exceeding that of natural photosynthetic systems.
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Affiliation(s)
- Chong Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Brendan C Colón
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marika Ziesack
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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18
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Abstract
We have known for 40 years that soils can consume the trace amounts of molecular hydrogen (H2) found in the Earth’s atmosphere.This process is predicted to be the most significant term in the global hydrogen cycle. However, the organisms and enzymes responsible for this process were only recently identified. Pure culture experiments demonstrated that several species of Actinobacteria, including streptomycetes and mycobacteria, can couple the oxidation of atmospheric H2 to the reduction of ambient O2. A combination of genetic, biochemical, and phenotypic studies suggest that these organisms primarily use this fuel source to sustain electron input into the respiratory chain during energy starvation. This process is mediated by a specialized enzyme, the group 5 [NiFe]-hydrogenase, which is unusual for its high affinity, oxygen insensitivity, and thermostability. Atmospheric hydrogen scavenging is a particularly dependable mode of energy generation, given both the ubiquity of the substrate and the stress tolerance of its catalyst. This minireview summarizes the recent progress in understanding how and why certain organisms scavenge atmospheric H2. In addition, it provides insight into the wider significance of hydrogen scavenging in global H2 cycling and soil microbial ecology.
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19
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Radu V, Frielingsdorf S, Lenz O, Jeuken LJC. Reactivation from the Ni–B state in [NiFe] hydrogenase of Ralstonia eutropha is controlled by reduction of the superoxidised proximal cluster. Chem Commun (Camb) 2016; 52:2632-5. [DOI: 10.1039/c5cc10382g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tolerance towards oxic conditions of O2-tolerant [NiFe] hydrogenases has been attributed to an unusual [4Fe–3S] cluster that lies proximal to the [NiFe] active site.
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Affiliation(s)
- Valentin Radu
- School of Biomedical Sciences
- The Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds LS2 9JT
- UK
| | - Stefan Frielingsdorf
- Institut für Chemie
- Sekretariat PC14
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Oliver Lenz
- Institut für Chemie
- Sekretariat PC14
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Lars J. C. Jeuken
- School of Biomedical Sciences
- The Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds LS2 9JT
- UK
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20
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Noth J, Kositzki R, Klein K, Winkler M, Haumann M, Happe T. Lyophilization protects [FeFe]-hydrogenases against O2-induced H-cluster degradation. Sci Rep 2015; 5:13978. [PMID: 26364994 PMCID: PMC4568494 DOI: 10.1038/srep13978] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/29/2015] [Indexed: 12/26/2022] Open
Abstract
Nature has developed an impressive repertoire of metal-based enzymes that perform complex chemical reactions under moderate conditions. Catalysts that produce molecular hydrogen (H2) are particularly promising for renewable energy applications. Unfortunately, natural and chemical H2-catalysts are often irreversibly degraded by molecular oxygen (O2). Here we present a straightforward procedure based on freeze-drying (lyophilization), that turns [FeFe]-hydrogenases, which are excellent H2-producers, but typically extremely O2-sensitive in solution, into enzymes that are fully resistant against O2. Complete dryness protects and conserves both, the [FeFe]-hydrogenase proteins and their inorganic active-site cofactor (H-cluster), when exposed to 100% O2 for days. The full H2-formation capacity is restored after solvation of the lyophilized enzymes. However, even minimal moisturizing re-establishes O2-sensitivity. The dry [FeFe]-hydrogenase material is superior also for advanced spectroscopic investigations on the H-cluster reaction mechanism. Our method provides a convenient way for long-term storage and impacts on potential biotechnological hydrogen production applications of hydrogenase enzymes.
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Affiliation(s)
- Jens Noth
- Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, 44801 Bochum, Germany
| | - Ramona Kositzki
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Kathrin Klein
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Anorganische Chemie I-Bioanorganische Chemie, 44801 Bochum, Germany
| | - Martin Winkler
- Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, 44801 Bochum, Germany
| | - Michael Haumann
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Thomas Happe
- Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, 44801 Bochum, Germany
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21
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Löwenstein J, Lauterbach L, Teutloff C, Lenz O, Bittl R. Active Site of the NAD(+)-Reducing Hydrogenase from Ralstonia eutropha Studied by EPR Spectroscopy. J Phys Chem B 2015. [PMID: 26214595 DOI: 10.1021/acs.jpcb.5b04144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pulsed ENDOR and HYSCORE measurements were carried out to characterize the active site of the oxygen-tolerant NAD(+)-reducing hydrogenase of Ralstonia eutropha. The catalytically active Nia-C state exhibits a bridging hydride between iron and nickel in the active site, which is photodissociated upon illumination. Its hyperfine coupling is comparable to that of standard hydrogenases. In addition, a histidine residue could be identified, which shows hyperfine and nuclear quadrupole parameters in significant variance from comparable histidine residues that are conserved in standard [NiFe] hydrogenases, and might be related to the O2 tolerance of the enzyme.
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Affiliation(s)
- Julia Löwenstein
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Lars Lauterbach
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Teutloff
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Robert Bittl
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
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22
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Ash PA, Liu J, Coutard N, Heidary N, Horch M, Gudim I, Simler T, Zebger I, Lenz O, Vincent KA. Electrochemical and Infrared Spectroscopic Studies Provide Insight into Reactions of the NiFe Regulatory Hydrogenase from Ralstonia eutropha with O2 and CO. J Phys Chem B 2015; 119:13807-15. [PMID: 26115011 DOI: 10.1021/acs.jpcb.5b04164] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulatory hydrogenase (RH) from Ralstonia eutropha acts as the H2-sensing unit of a two-component system that regulates biosynthesis of the energy conserving hydrogenases of the organism according to the availability of H2. The H2 oxidation activity, which was so far determined in vitro with artificial electron acceptors, has been considered to be insensitive to O2 and CO. It is assumed that bulky isoleucine and phenylalanine amino acid residues close to the NiFe active site "gate" gas access, preventing molecules larger than H2 interacting with the active site. We have carried out sensitive electrochemical measurements to demonstrate that O2 is in fact an inhibitor of H2 oxidation by the RH, and that both H(+) reduction and H2 oxidation are inhibited by CO. Furthermore, we have demonstrated that the inhibitory effect of O2 arises due to interaction of O2 with the active site. Using protein film infrared electrochemistry (PFIRE) under H2 oxidation conditions, in conjunction with solution infrared measurements, we have identified previously unreported oxidized inactive and catalytically active reduced states of the RH active site. These findings suggest that the RH has a rich active site chemistry similar to that of other NiFe hydrogenases.
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Affiliation(s)
- Philip A Ash
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Juan Liu
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nathan Coutard
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nina Heidary
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Marius Horch
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Ingvild Gudim
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Thomas Simler
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Kylie A Vincent
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
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23
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Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment. Curr Microbiol 2015; 71:296-302. [PMID: 26044993 PMCID: PMC4486115 DOI: 10.1007/s00284-015-0846-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/19/2015] [Indexed: 11/13/2022]
Abstract
Many promising hydrogen technologies utilising hydrogenase enzymes have been slowed by the fact that most hydrogenases are extremely sensitive to O2. Within the group 1 membrane-bound NiFe hydrogenase, naturally occurring tolerant enzymes do exist, and O2 tolerance has been largely attributed to changes in iron–sulphur clusters coordinated by different numbers of cysteine residues in the enzyme’s small subunit. Indeed, previous work has provided a robust phylogenetic signature of O2 tolerance [1], which when combined with new sequencing technologies makes bio prospecting in nature a far more viable endeavour. However, making sense of such a vast diversity is still challenging and could be simplified if known species with O2-tolerant enzymes were annotated with information on metabolism and natural environments. Here, we utilised a bioinformatics approach to compare O2-tolerant and sensitive membrane-bound NiFe hydrogenases from 177 bacterial species with fully sequenced genomes for differences in their taxonomy, O2 requirements, and natural environment. Following this, we interrogated a metagenome from lacustrine surface sediment for novel hydrogenases via high-throughput shotgun DNA sequencing using the Illumina™ MiSeq platform. We found 44 new NiFe group 1 membrane-bound hydrogenase sequence fragments, five of which segregated with the tolerant group on the phylogenetic tree of the enzyme’s small subunit, and four with the large subunit, indicating de novo O2-tolerant protein sequences that could help engineer more efficient hydrogenases.
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24
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Wawrousek K, Noble S, Korlach J, Chen J, Eckert C, Yu J, Maness PC. Genome annotation provides insight into carbon monoxide and hydrogen metabolism in Rubrivivax gelatinosus. PLoS One 2014; 9:e114551. [PMID: 25479613 PMCID: PMC4257681 DOI: 10.1371/journal.pone.0114551] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/10/2014] [Indexed: 12/25/2022] Open
Abstract
We report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS. This microbe is a model for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO2 and H2 as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and hydrogenase. As expected, analysis of the genome of Rx. gelatinosus CBS reveals the presence of genes encoding both enzyme complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional hydrogenases, an uptake hydrogenase that liberates the electrons in H2 in support of cell growth, and a regulatory hydrogenase that senses H2 and relays the signal to a two-component system that ultimately controls synthesis of the uptake hydrogenase. The genome also contains two sets of hydrogenase maturation genes which are known to assemble the catalytic metallocluster of the hydrogenase NiFe active site. Collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables Rx. gelatinosus CBS to thrive on CO or H2 in support of cell growth.
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Affiliation(s)
- Karen Wawrousek
- Department of Chemical and Petroleum Engineering, University of Wyoming, Laramie, Wyoming, United States of America
| | - Scott Noble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Jin Chen
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Carrie Eckert
- Department of Chemical and Petroleum Engineering, University of Wyoming, Laramie, Wyoming, United States of America
| | - Jianping Yu
- Department of Chemical and Petroleum Engineering, University of Wyoming, Laramie, Wyoming, United States of America
| | - Pin-Ching Maness
- Department of Chemical and Petroleum Engineering, University of Wyoming, Laramie, Wyoming, United States of America
- * E-mail:
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25
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Liu C, Liu T, Hall MB. Influence of the Density Functional and Basis Set on the Relative Stabilities of Oxygenated Isomers of Diiron Models for the Active Site of [FeFe]-Hydrogenase. J Chem Theory Comput 2014; 11:205-14. [DOI: 10.1021/ct500594z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Caiping Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
- State
Key Laboratory of Structure Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, P. R. China, 350002
| | - Tianbiao Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
- Energy
Processes and Materials Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Michael B. Hall
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
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26
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So K, Kitazumi Y, Shirai O, Kurita K, Nishihara H, Higuchi Y, Kano K. Kinetic Analysis of Inactivation and Enzyme Reaction of Oxygen-Tolerant [NiFe]-Hydrogenase at Direct Electron-Transfer Bioanode. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20140223] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Keisei So
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Yuki Kitazumi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Osamu Shirai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST)
| | - Kouhei Kurita
- Department of Bioresource Science, Collage of Agriculture, Ibaraki University
| | - Hirofumi Nishihara
- Department of Bioresource Science, Collage of Agriculture, Ibaraki University
| | - Yoshiki Higuchi
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST)
- Department of Life Science, Graduate School of Life Science, University of Hyogo
| | - Kenji Kano
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST)
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27
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Finkelmann AR, Stiebritz MT, Reiher M. Activation Barriers of Oxygen Transformation at the Active Site of [FeFe] Hydrogenases. Inorg Chem 2014; 53:11890-902. [DOI: 10.1021/ic501049z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arndt R. Finkelmann
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Martin T. Stiebritz
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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28
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So K, Kitazumi Y, Shirai O, Kurita K, Nishihara H, Higuchi Y, Kano K. Gas-diffusion and Direct-electron-transfer-type Bioanode for Hydrogen Oxidation with Oxygen-tolerant [NiFe]-hydrogenase as an Electrocatalyst. CHEM LETT 2014. [DOI: 10.1246/cl.140622] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Keisei So
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Yuki Kitazumi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Osamu Shirai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST)
| | - Kouhei Kurita
- Department of Bioresource Science, College of Agriculture, Ibaraki University
| | - Hirofumi Nishihara
- Department of Bioresource Science, College of Agriculture, Ibaraki University
| | - Yoshiki Higuchi
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST)
- Department of Life Science, Graduate School of Life Science, University of Hyogo
| | - Kenji Kano
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST)
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29
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Albareda M, Pacios LF, Manyani H, Rey L, Brito B, Imperial J, Ruiz-Argüeso T, Palacios JM. Maturation of Rhizobium leguminosarum hydrogenase in the presence of oxygen requires the interaction of the chaperone HypC and the scaffolding protein HupK. J Biol Chem 2014; 289:21217-29. [PMID: 24942742 DOI: 10.1074/jbc.m114.577403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
[NiFe] hydrogenases are key enzymes for the energy and redox metabolisms of different microorganisms. Synthesis of these metalloenzymes involves a complex series of biochemical reactions catalyzed by a plethora of accessory proteins, many of them required to synthesize and insert the unique NiFe(CN)2CO cofactor. HypC is an accessory protein conserved in all [NiFe] hydrogenase systems and involved in the synthesis and transfer of the Fe(CN)2CO cofactor precursor. Hydrogenase accessory proteins from bacteria-synthesizing hydrogenase in the presence of oxygen include HupK, a scaffolding protein with a moderate sequence similarity to the hydrogenase large subunit and proposed to participate as an intermediate chaperone in the synthesis of the NiFe cofactor. The endosymbiotic bacterium Rhizobium leguminosarum contains a single hydrogenase system that can be expressed under two different physiological conditions: free-living microaerobic cells (∼ 12 μm O2) and bacteroids from legume nodules (∼ 10-100 nm O2). We have used bioinformatic tools to model HupK structure and interaction of this protein with HypC. Site-directed mutagenesis at positions predicted as critical by the structural analysis have allowed the identification of HupK and HypC residues relevant for the maturation of hydrogenase. Mutant proteins altered in some of these residues show a different phenotype depending on the physiological condition tested. Modeling of HypC also predicts the existence of a stable HypC dimer whose presence was also demonstrated by immunoblot analysis. This study widens our understanding on the mechanisms for metalloenzyme biosynthesis in the presence of oxygen.
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Affiliation(s)
- Marta Albareda
- From the Centro de Biotecnología y Genómica de Plantas and Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Luis F Pacios
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros de Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain, and
| | - Hamid Manyani
- From the Centro de Biotecnología y Genómica de Plantas and Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Luis Rey
- From the Centro de Biotecnología y Genómica de Plantas and Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Belén Brito
- From the Centro de Biotecnología y Genómica de Plantas and Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Juan Imperial
- From the Centro de Biotecnología y Genómica de Plantas and Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain, Consejo Superior de Investigaciones Científicas, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Tomás Ruiz-Argüeso
- From the Centro de Biotecnología y Genómica de Plantas and Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Jose M Palacios
- From the Centro de Biotecnología y Genómica de Plantas and Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain,
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30
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Radu V, Frielingsdorf S, Evans SD, Lenz O, Jeuken LJC. Enhanced oxygen-tolerance of the full heterotrimeric membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha. J Am Chem Soc 2014; 136:8512-5. [PMID: 24866391 PMCID: PMC4073834 DOI: 10.1021/ja503138p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hydrogenases are oxygen-sensitive enzymes that catalyze the conversion between protons and hydrogen. Water-soluble subcomplexes of membrane-bound [NiFe]-hydrogenases (MBH) have been extensively studied for applications in hydrogen-oxygen fuel cells as they are relatively tolerant to oxygen, although even these catalysts are still inactivated in oxidative conditions. Here, the full heterotrimeric MBH of Ralstonia eutropha, including the membrane-integral cytochrome b subunit, was investigated electrochemically using electrodes modified with planar tethered bilayer lipid membranes (tBLM). Cyclic voltammetry and chronoamperometry experiments show that MBH, in equilibrium with the quinone pool in the tBLM, does not anaerobically inactivate under oxidative redox conditions. In aerobic environments, the MBH is reversibly inactivated by O2, but reactivation was found to be fast even under oxidative redox conditions. This enhanced resistance to inactivation is ascribed to the oligomeric state of MBH in the lipid membrane.
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Affiliation(s)
- Valentin Radu
- School of Biomedical Sciences, the Astbury Centre for Structural Molecular Biology, and School of Physics & Astronomy, University of Leeds , Leeds LS2 9JT, United Kingdom
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31
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 624] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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32
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Frielingsdorf S, Fritsch J, Schmidt A, Hammer M, Löwenstein J, Siebert E, Pelmenschikov V, Jaenicke T, Kalms J, Rippers Y, Lendzian F, Zebger I, Teutloff C, Kaupp M, Bittl R, Hildebrandt P, Friedrich B, Lenz O, Scheerer P. Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase. Nat Chem Biol 2014; 10:378-85. [DOI: 10.1038/nchembio.1500] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 03/13/2014] [Indexed: 12/27/2022]
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33
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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34
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Bruschi M, Tiberti M, Guerra A, De Gioia L. Disclosure of Key Stereoelectronic Factors for Efficient H2 Binding and Cleavage in the Active Site of [NiFe]-Hydrogenases. J Am Chem Soc 2014; 136:1803-14. [DOI: 10.1021/ja408511y] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Maurizio Bruschi
- Department
of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza
della Scienza 1, 20126-Milan, Italy
| | - Matteo Tiberti
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126-Milan, Italy
| | - Alessandro Guerra
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126-Milan, Italy
| | - Luca De Gioia
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126-Milan, Italy
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35
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Fritsch J, Siebert E, Priebe J, Zebger I, Lendzian F, Teutloff C, Friedrich B, Lenz O. Rubredoxin-related maturation factor guarantees metal cofactor integrity during aerobic biosynthesis of membrane-bound [NiFe] hydrogenase. J Biol Chem 2014; 289:7982-93. [PMID: 24448806 DOI: 10.1074/jbc.m113.544668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane-bound [NiFe] hydrogenase (MBH) supports growth of Ralstonia eutropha H16 with H2 as the sole energy source. The enzyme undergoes a complex biosynthesis process that proceeds during cell growth even at ambient O2 levels and involves 14 specific maturation proteins. One of these is a rubredoxin-like protein, which is essential for biosynthesis of active MBH at high oxygen concentrations but dispensable under microaerobic growth conditions. To obtain insights into the function of HoxR, we investigated the MBH protein purified from the cytoplasmic membrane of hoxR mutant cells. Compared with wild-type MBH, the mutant enzyme displayed severely decreased hydrogenase activity. Electron paramagnetic resonance and infrared spectroscopic analyses revealed features resembling those of O2-sensitive [NiFe] hydrogenases and/or oxidatively damaged protein. The catalytic center resided partially in an inactive Niu-A-like state, and the electron transfer chain consisting of three different Fe-S clusters showed marked alterations compared with wild-type enzyme. Purification of HoxR protein from its original host, R. eutropha, revealed only low protein amounts. Therefore, recombinant HoxR protein was isolated from Escherichia coli. Unlike common rubredoxins, the HoxR protein was colorless, rather unstable, and essentially metal-free. Conversion of the atypical iron-binding motif into a canonical one through genetic engineering led to a stable reddish rubredoxin. Remarkably, the modified HoxR protein did not support MBH-dependent growth at high O2. Analysis of MBH-associated protein complexes points toward a specific interaction of HoxR with the Fe-S cluster-bearing small subunit. This supports the previously made notion that HoxR avoids oxidative damage of the metal centers of the MBH, in particular the unprecedented Cys6[4Fe-3S] cluster.
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Affiliation(s)
- Johannes Fritsch
- From the Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin
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36
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Engineering Hydrogenases for H2 Production: Bolts and Goals. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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37
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Abstract
The origin of the tolerance of a subclass of [NiFe]-hydrogenases to the presence of oxygen was unclear for a long time. Recent spectroscopic studies showed a conserved active site between oxygen-sensitive and oxygen-tolerant hydrogenases, and modifications in the vicinity of the active site in the large subunit could be excluded as the origin of catalytic activity even in the presence of molecular oxygen. A combination of bioinformatics and protein structural modelling revealed an unusual co-ordination motif in the vicinity of the proximal Fe-S cluster in the small subunit. Mutational experiments confirmed the relevance of two additional cysteine residues for the oxygen-tolerance. This new binding motif can be used to classify sequences from [NiFe]-hydrogenases according to their potential oxygen-tolerance. The X-ray structural analysis of the reduced form of the enzyme displayed a new type of [4Fe-3S] cluster co-ordinated by six surrounding cysteine residues in a distorted cubanoid geometry. The unusual electronic structure of the proximal Fe-S cluster can be analysed using the broken-symmetry approach and gave results in agreement with experimental Mößbauer studies. An electronic effect of the proximal Fe-S cluster on the remote active site can be detected and quantified. In the oxygen-tolerant hydrogenases, the hydride occupies an asymmetric binding position in the Ni-C state. This may rationalize the more facile activation and catalytic turnover in this subclass of enzymes.
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38
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Ataka K, Stripp ST, Heberle J. Surface-enhanced infrared absorption spectroscopy (SEIRAS) to probe monolayers of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2283-93. [PMID: 23816441 DOI: 10.1016/j.bbamem.2013.04.026] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/05/2013] [Accepted: 04/28/2013] [Indexed: 12/15/2022]
Abstract
Surface-enhanced infrared absorption spectroscopy (SEIRAS) represents a variation of conventional infrared spectroscopy and exploits the signal enhancement exerted by the plasmon resonance of nano-structured metal thin films. The surface enhancement decays in about 10nm with the distance from the surface and is, thus, perfectly suited to selectively probe monolayers of biomembranes. Peculiar to membrane proteins is their vectorial functionality, the probing of which requires proper orientation within the membrane. To this end, the metal surface used in SEIRAS is chemically modified to generate an oriented membrane protein film. Monolayers of uniformly oriented membrane proteins are formed by tethering His-tagged proteins to a nickel nitrilo-triacetic acid (Ni-NTA) modified gold surface and SEIRAS commands molecular sensitivity to probe each step of surface modification. The solid surface used as plasmonic substrate for SEIRAS, can also be employed as an electrode to investigate systems where electron transfer reactions are relevant, like e.g. cytochrome c oxidase or plant-type photosystems. Furthermore, the interaction of these membrane proteins with water-soluble proteins, like cytochrome c or hydrogenase, is studied on the molecular level by SEIRAS. The impact of the membrane potential on protein functionality is verified by monitoring light-dark difference spectra of a monolayer of sensory rhodopsin (SRII) at different applied potentials. It is demonstrated that the interpretations of all of these experiments critically depend on the orientation of the solid-supported membrane protein. Finally, future directions of SEIRAS including cellular systems are discussed. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Kenichi Ataka
- Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
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39
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Novel, oxygen-insensitive group 5 [NiFe]-hydrogenase in Ralstonia eutropha. Appl Environ Microbiol 2013; 79:5137-45. [PMID: 23793632 DOI: 10.1128/aem.01576-13] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, a novel group of [NiFe]-hydrogenases has been defined that appear to have a great impact in the global hydrogen cycle. This so-called group 5 [NiFe]-hydrogenase is widespread in soil-living actinobacteria and can oxidize molecular hydrogen at atmospheric levels, which suggests a high affinity of the enzyme toward H2. Here, we provide a biochemical characterization of a group 5 hydrogenase from the betaproteobacterium Ralstonia eutropha H16. The hydrogenase was designated an actinobacterial hydrogenase (AH) and is catalytically active, as shown by the in vivo H2 uptake and by activity staining in native gels. However, the enzyme does not sustain autotrophic growth on H2. The AH was purified to homogeneity by affinity chromatography and consists of two subunits with molecular masses of 65 and 37 kDa. Among the electron acceptors tested, nitroblue tetrazolium chloride was reduced by the AH at highest rates. At 30°C and pH 8, the specific activity of the enzyme was 0.3 μmol of H2 per min and mg of protein. However, an unexpectedly high Michaelis constant (Km) for H2 of 3.6 ± 0.5 μM was determined, which is in contrast to the previously proposed low Km of group 5 hydrogenases and makes atmospheric H2 uptake by R. eutropha most unlikely. Amperometric activity measurements revealed that the AH maintains full H2 oxidation activity even at atmospheric oxygen concentrations, showing that the enzyme is insensitive toward O2.
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40
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Nonaka K, Nguyen NT, Yoon KS, Ogo S. Novel H2-oxidizing [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F. J Biosci Bioeng 2013. [DOI: 10.1016/j.jbiosc.2012.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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[NiFe] hydrogenases: a common active site for hydrogen metabolism under diverse conditions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:986-1002. [PMID: 23399489 DOI: 10.1016/j.bbabio.2013.01.015] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/06/2012] [Accepted: 01/26/2013] [Indexed: 01/05/2023]
Abstract
Hydrogenase proteins catalyze the reversible conversion of molecular hydrogen to protons and electrons. The most abundant hydrogenases contain a [NiFe] active site; these proteins are generally biased towards hydrogen oxidation activity and are reversibly inhibited by oxygen. However, there are [NiFe] hydrogenase that exhibit unique properties, including aerobic hydrogen oxidation and preferential hydrogen production activity; these proteins are highly relevant in the context of biotechnological devices. This review describes four classes of these "nonstandard" [NiFe] hydrogenases and discusses the electrochemical, spectroscopic, and structural studies that have been used to understand the mechanisms behind this exceptional behavior. A revised classification protocol is suggested in the conclusions, particularly with respect to the term "oxygen-tolerance". This article is part of a special issue entitled: metals in bioenergetics and biomimetics systems.
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42
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Kim JYH, Cha HJ. Recent progress in hydrogenase and its biotechnological application for viable hydrogen technology. KOREAN J CHEM ENG 2013. [DOI: 10.1007/s11814-012-0208-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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43
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44
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De Poulpiquet A, Ciaccafava A, Szot K, Pillain B, Infossi P, Guiral M, Opallo M, Giudici-Orticoni MT, Lojou E. Exploring Properties of a Hyperthermophilic Membrane-Bound Hydrogenase at Carbon Nanotube Modified Electrodes for a Powerful H2/O2Biofuel Cell. ELECTROANAL 2013. [DOI: 10.1002/elan.201200405] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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45
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Oda T, Oda K, Yamamoto H, Matsuyama A, Ishii M, Igarashi Y, Nishihara H. Hydrogen-driven asymmetric reduction of hydroxyacetone to (R)-1,2-propanediol by Ralstonia eutropha transformant expressing alcohol dehydrogenase from Kluyveromyces lactis. Microb Cell Fact 2013; 12:2. [PMID: 23305396 PMCID: PMC3552938 DOI: 10.1186/1475-2859-12-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 01/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Conversion of industrial processes to more nature-friendly modes is a crucial subject for achieving sustainable development. Utilization of hydrogen-oxidation reactions by hydrogenase as a driving force of bioprocess reaction can be an environmentally ideal method because the reaction creates no pollutants. We expressed NAD-dependent alcohol dehydrogenase from Kluyveromyces lactis in a hydrogen-oxidizing bacterium: Ralstonia eutropha. This is the first report of hydrogen-driven in vivo coupling reaction of the alcohol dehydrogenase and indigenous soluble NAD-reducing hydrogenase. Asymmetric reduction of hydroxyacetone to (R)-1,2-propanediol, which is a commercial building block for antibacterial agents, was performed using the transformant as the microbial cell catalyst. RESULTS The two enzymes coupled in vitro in vials without a marked decrease of reactivity during the 20 hr reaction because of the hydrogenase reaction, which generates no by-product that affects enzymes. Alcohol dehydrogenase was expressed functionally in R. eutropha in an activity level equivalent to that of indigenous NAD-reducing hydrogenase under the hydrogenase promoter. The hydrogen-driven in vivo coupling reaction proceeded only by the transformant cell without exogenous addition of a cofactor. The decrease of reaction velocity at higher concentration of hydroxyacetone was markedly reduced by application of an in vivo coupling system. Production of (R)-1,2-propanediol (99.8% e.e.) reached 67.7 g/l in 76 hr with almost a constant rate using a jar fermenter. The reaction velocity under 10% PH2 was almost equivalent to that under 100% hydrogen, indicating the availability of crude hydrogen gas from various sources. The in vivo coupling system enabled cell-recycling as catalysts. CONCLUSIONS Asymmetric reduction of hydroxyacetone by a coupling reaction of the two enzymes continued in both in vitro and in vivo systems in the presence of hydrogen. The in vivo reaction system using R. eutropha transformant expressing heterologous alcohol dehydrogenase showed advantages for practical usage relative to the in vitro coupling system. The results suggest a hopeful perspective of the hydrogen-driven bioprocess as an environmentally outstanding method to achieve industrial green innovation. Hydrogen-oxidizing bacteria can be useful hosts for the development of hydrogen-driven microbial cell factories.
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Affiliation(s)
- Takahiro Oda
- Department of Bioresource Science, College of Agriculture, Ibaraki University, 3-21-1 Chu-ou, Ami-machi, Inashiki-gun, Ibaraki, 300-0393, Japan
| | - Koji Oda
- Department of Bioresource Science, College of Agriculture, Ibaraki University, 3-21-1 Chu-ou, Ami-machi, Inashiki-gun, Ibaraki, 300-0393, Japan
| | - Hiroaki Yamamoto
- Green Product Development Center, R&D Management, Daicel Corporation, 1-1 Shinko-cho, Myoko, Niigata, 944-8550, Japan
| | - Akinobu Matsuyama
- Green Product Development Center, R&D Management, Daicel Corporation, 1-1 Shinko-cho, Myoko, Niigata, 944-8550, Japan
| | - Masaharu Ishii
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuo Igarashi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hirofumi Nishihara
- Department of Bioresource Science, College of Agriculture, Ibaraki University, 3-21-1 Chu-ou, Ami-machi, Inashiki-gun, Ibaraki, 300-0393, Japan
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46
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Mouesca JM, Fontecilla-Camps JC, Amara P. The Structural Plasticity of the Proximal [4Fe3S] Cluster is Responsible for the O2Tolerance of Membrane-Bound [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2013; 52:2002-6. [DOI: 10.1002/anie.201209063] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Indexed: 11/08/2022]
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47
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Mouesca JM, Fontecilla-Camps JC, Amara P. The Structural Plasticity of the Proximal [4Fe3S] Cluster is Responsible for the O2
Tolerance of Membrane-Bound [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kim K, Kishima T, Matsumoto T, Nakai H, Ogo S. Selective Redox Activation of H2 or O2 in a [NiRu] Complex by Aromatic Ligand Effects. Organometallics 2012. [DOI: 10.1021/om300833m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Kyoungmok Kim
- International Institute for Carbon-Neutral
Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku,
Fukuoka 819-0395, Japan
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahiro Kishima
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral
Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku,
Fukuoka 819-0395, Japan
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hidetaka Nakai
- International Institute for Carbon-Neutral
Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku,
Fukuoka 819-0395, Japan
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral
Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku,
Fukuoka 819-0395, Japan
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
- Core Research for
Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi
Center Building, 4-1-8 Honcho, Kawaguchi-shi, Saitama
332-0012, Japan
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Relation between anaerobic inactivation and oxygen tolerance in a large series of NiFe hydrogenase mutants. Proc Natl Acad Sci U S A 2012; 109:19916-21. [PMID: 23169623 DOI: 10.1073/pnas.1212258109] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nickel-containing hydrogenases, the biological catalysts of oxidation and production, reversibly inactivate under anaerobic, oxidizing conditions. We aim at understanding the mechanism of (in)activation and what determines its kinetics, because there is a correlation between fast reductive reactivation and oxygen tolerance, a property of some hydrogenases that is very desirable from the point of view of biotechnology. Direct electrochemistry is potentially very useful for learning about the redox-dependent conversions between active and inactive forms of hydrogenase, but the voltammetric signals are complex and often misread. Here we describe simple analytical models that we used to characterize and compare 16 mutants, obtained by substituting the position-74 valine of the -sensitive NiFe hydrogenase from Desulfovibrio fructosovorans. We observed that this substitution can accelerate reactivation up to 1,000-fold, depending on the polarity of the position 74 amino acid side chain. In terms of kinetics of anaerobic (in)activation and oxygen tolerance, the valine-to-histidine mutation has the most spectacular effect: The V74H mutant compares favorably with the -tolerant hydrogenase from Aquifex aeolicus, which we use here as a benchmark.
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50
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Greene BL, Joseph CA, Maroney MJ, Dyer RB. Direct evidence of active-site reduction and photodriven catalysis in sensitized hydrogenase assemblies. J Am Chem Soc 2012; 134:11108-11. [PMID: 22716776 DOI: 10.1021/ja3042367] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report photocatalytic H(2) production by hydrogenase (H(2)ase)-quantum dot (QD) hybrid assemblies. Quenching of the CdTe exciton emission was observed, consistent with electron transfer from the quantum dot to H(2)ase. GC analysis showed light-driven H(2) production in the presence of a sacrificial electron donor with an efficiency of 4%, which is likely a lower limit for these hybrid systems. FTIR spectroscopy was employed for direct observation of active-site reduction in unprecedented detail for photodriven H(2)ase catalysis with sensitivity toward both H(2)ase and the sacrificial electron donor. Photosensitization with Ru(bpy)(3)(2+) showed distinct FTIR photoreduction properties, generating all of the states along the steady-state catalytic cycle with minimal H(2) production, indicating slow, sequential one-electron reduction steps. Comparing the H(2)ase activity and FTIR results for the two systems showed that QDs bind more efficiently for electron transfer and that the final enzyme state is different for the two sensitizers. The possible origins of these differences and their implications for the enzymatic mechanism are discussed.
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Affiliation(s)
- Brandon L Greene
- Chemistry Department, Emory University, Atlanta, Georgia 30322, USA
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